Dengue disease is caused by 4 antigenically distinct serotypes of dengue virus (DENV-1-4) transmitted by Aedes mosquitoes, principally Aedes aegypti. Dengue disease affects 50-100 million people annually, causing 25,000 deaths and more than a half-million hospitalizations. Dengue is endemic or sporadic in >100 countries worldwide; Aedes aegypti inhabits tropical and subtropical regions and some temperate areas, and its range is expanding. Dengue virus can cause a continuum of disease: dengue fever causes biphasic fever, rash, extreme muscle or joint pain, headache, and eye pain; dengue hemorrhagic fever causes abnormal homeostasis and increased vascular permeability, with severe cases leading to dengue shock syndrome. Exposure generates life-long, serotype-specific immunity, but subsequent infections with other serotypes may increase the risk of severe disease. Complex disease presentation and sudden development of hemorrhagic symptoms in seemingly stable patients can cause fatal outcomes even in well-prepared hospitals. No vaccine or treatment exists; mosquito control and personal protection are the primary defenses. The scale of the problem and the cost of protective measures make vaccine development a public health priority.
Antigenic variability is a major reason preventing development of efficient vaccines against DENV as well as against other highly variable pathogens (e.g., viral pathogens from the Retroviridae, Picornaviridae, Caliciviridae, Togaviridae, Flaviridae, Coronaviridae, Rhabdoviridae, Filoviridae, Paramyxoviridae, Orthomyxoviridae, Bunyaviridae, Arena viridae, Reoviridae, Birnaviridae, Hepadnaviridae, Parvoviridae, Papovaviridae, Adenoviridae, Herperviridae, Poxyiridae, and Iridoviridae families). Current approaches focus on regular reformulation of vaccines (such as influenza), combining multiple variants (such as influenza or HPV), or using existing vaccines that provide variable levels of protection (e.g., rotavirus, yellow fever). For most viral diseases in humans, however, currently vaccines are not available.
Epitope-based vaccines against highly-variable viral pathogens require broad coverage. Traditional approaches to assembling broadly covering sets of peptides are commonly based on assembling highly conserved peptides—i.e. peptides present in a given fraction of the viral population (typically 90% or higher). Therefore, it is often observed that low frequency peptides are purposely omitted from vaccine designs, despite the fact that low frequency antigenic peptides can be excellent immunogens and when combined with high frequency peptides could therefore provide broader coverage of viral variants and, therefore, more effective vaccines. There therefore exists a need in the art to provide methods for identifying novel peptidic targets for immunogenic compositions, such as vaccines and immunotherapies. This invention addresses these and other needs as described in detail below.